vocab updated to ontology

src/ontology/imports/iao_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://si.eu-parc.eu//pko/imports/iao_import.owl>
-<http://si.eu-parc.eu//pko/releases/2023-09-03/imports/iao_import.owl>
+<http://si.eu-parc.eu//pko/releases/2023-11-13/imports/iao_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/iao/2022-11-07/iao.owl>)
-Annotation(owl:versionInfo "2023-09-03")
+Annotation(owl:versionInfo "2023-11-13")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
@@ -26,7 +26,9 @@ Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000030>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000078>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000102>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000225>))
+Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000300>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000409>))
+Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000605>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/IAO_0000136>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000052>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>))
@@ -79,6 +81,62 @@ Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
 Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
+############################
+#   Annotation Properties
+############################
+
+# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000115> (definition)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000115> "definition"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000115> "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/IAO_0000115> "2012-04-05: 
+Barry Smith
+
+The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions'  is terrible.
+
+Can you fix to something like:
+
+A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
+
+Alan Ruttenberg
+
+Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. 
+
+On the specifics of the proposed definition:
+
+We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. 
+
+Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. 
+
+We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.  "@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000115> "PERSON:Daniel Schober"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000115> "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"@en)
+AnnotationAssertion(rdfs:isDefinedBy <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/iao.owl>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "definition"@en)
+
+# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000117> (term editor)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000117> "term editor"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000117> "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/IAO_0000117> "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000117> "PERSON:Daniel Schober"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000117> "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"@en)
+AnnotationAssertion(rdfs:isDefinedBy <http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/iao.owl>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000117> "term editor"@en)
+
+# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000119> (definition source)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000119> "definition source"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000119> "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000119> "PERSON:Daniel Schober"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000119> "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/IAO_0000119> "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"@en)
+AnnotationAssertion(rdfs:isDefinedBy <http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/iao.owl>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000119> "definition source"@en)
+
 
 ############################
 #   Object Properties
@@ -472,6 +530,19 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000225> "obs
 EquivalentClasses(<http://purl.obolibrary.org/obo/IAO_0000225> ObjectOneOf(<http://purl.obolibrary.org/obo/IAO_0000103> <http://purl.obolibrary.org/obo/IAO_0000226> <http://purl.obolibrary.org/obo/IAO_0000227> <http://purl.obolibrary.org/obo/IAO_0000228> <http://purl.obolibrary.org/obo/IAO_0000229> <http://purl.obolibrary.org/obo/OMO_0001000>))
 SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000225> <http://purl.obolibrary.org/obo/IAO_0000102>)
 
+# Class: <http://purl.obolibrary.org/obo/IAO_0000300> (textual entity)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000300> "textual entity"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/IAO_0000300> "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/IAO_0000300> <http://purl.obolibrary.org/obo/IAO_0000123>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000300> "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/IAO_0000300> "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/IAO_0000300> "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000300> "PERSON: Lawrence Hunter"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/IAO_0000300> "text"@en)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000300> "textual entity"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000300> <http://purl.obolibrary.org/obo/IAO_0000030>)
+
 # Class: <http://purl.obolibrary.org/obo/IAO_0000409> (denotator type)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000409> "denotator type"@en)
@@ -483,6 +554,18 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000409> "den
 EquivalentClasses(<http://purl.obolibrary.org/obo/IAO_0000409> ObjectOneOf(<http://purl.obolibrary.org/obo/IAO_0000410> <http://purl.obolibrary.org/obo/IAO_0000420> <http://purl.obolibrary.org/obo/IAO_0000421>))
 SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000409> <http://purl.obolibrary.org/obo/IAO_0000102>)
 
+# Class: <http://purl.obolibrary.org/obo/IAO_0000605> (abbreviation textual entity)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000111> <http://purl.obolibrary.org/obo/IAO_0000605> "abbreviation textual entity"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000112> <http://purl.obolibrary.org/obo/IAO_0000605> "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):
+
+BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IAO_0000605> "A textual entity listing abbreviations and their expansions that are used in a document."@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/IAO_0000605> "PERSON: Bill Baumgartner"@en)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000233> <http://purl.obolibrary.org/obo/IAO_0000605> <https://github.com/information-artifact-ontology/IAO/issues/183>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000605> "abbreviation textual entity"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000605> <http://purl.obolibrary.org/obo/IAO_0000300>)
+
 
 ############################
 #   Named Individuals

src/ontology/imports/pato_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://si.eu-parc.eu//pko/imports/pato_import.owl>
-<http://si.eu-parc.eu//pko/releases/2023-09-03/imports/pato_import.owl>
+<http://si.eu-parc.eu//pko/releases/2023-11-13/imports/pato_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/pato/releases/2023-05-18/pato.owl>)
-Annotation(owl:versionInfo "2023-09-03")
+Annotation(owl:versionInfo "2023-11-13")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
@@ -192,6 +192,10 @@ Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#closeMatch>)
 #   Annotation Properties
 ############################
 
+# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000115> (definition)
+
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "definition")
+
 # Annotation Property: <http://purl.obolibrary.org/obo/RO_0002259> (<http://purl.obolibrary.org/obo/RO_0002259>)
 
 SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/RO_0002259> <http://www.geneontology.org/formats/oboInOwl#SubsetProperty>)

src/ontology/pko-odk.yaml

@@ -93,8 +93,8 @@ workflows:
   - docs
 components:
   products:
-    - filename: vocab.owl # TSV templates to define VIBSO classes
+    - filename: vocab.owl # 
       use_template: true
       template_options: --add-prefixes config/context.json
       templates:
-        - vocab.tsv # TSV templates to define VIBSO object properties
+        - vocab.tsv #